I suppose the real problem is, for many, JRPGs are not, in fact, RPGs.
We all know it's the category they're placed under, and when someone says "JRPG", we know what it's supposed to mean. But, for many, an RPG is, well, a role playing game. You take command of a character who has to act as an extension of you. You make decisions that affect the world you exist in as well as the character itself.
With many JRPGs, you generally are not making any decisions. You aren't the character you control, you simply take over for a small bit of free-roaming. You can make some decisions which may change a few dynamics of the game, but with a few truly notable exceptions, you simply are on the rails watching as the characters do everything for you.
Qualifying statements? Why, sure, I've got a whole bag of 'em right over here. Let me see...
Oooh, this one's got a little age on it, but it's nice and fragrant and reeks of the point I'm trying to make:
Final Fantasy VIII
I don't know about you, but if I were truly in control of Squall, I'd have just chucked most of the slow, whiny relationship with Rinoa and taken an eager and willing Quistis into my dorm room to see how many tricks she could think of with that whip. But instead of having steamy turn-based sex with my "teacher", I'm left to yell at Squall every time he soliloquises about his stupid fractured past and why he just plain don't trust people(Not in a cool, gritty old man kind of way, but in a desperately attention-seeking teenager kind of way). Nothing about Squall reflects me or any decisions I've made for him, and thus does not qualify as a role playing game. The story has the same ending no matter what I do, and none of my side-questing did anything to affect the outcome.
Ultimately, if I don't like the story, there's nothing I can do to affect my role in it. And with JRPGs, well, there are simply concepts that do not end up translating very well. By which I mean the actual translations.
Sure, we've come a long way from "All Your Base are Belong to Us", but the dialogue in a lot of JRPGs can range to boring and pointless to painful and bizarre. Which was much more acceptable when the characters could not audibly speak. Japan, for whatever reason, neither knows how english is supposed to sound naturally, nor can they find anyone who can comfortably speak Japanese enough to translate into decent(not "acceptable") dialogue. I've never played a JRPG and said to myself: "Ooh, that's a witty comeback" or "Wow, this really speaks to me". Because the best they can do, for the most part, is make the english understandable. But as soon as they accomplish that, they let the English-speaking producers hire their in-laws to do the voice acting, and everything becomes laughably terrible.
This isn't an old complaint by any means. I could probably name at least 5 JRPGs off the top of my head for our most recent console generation that suffer aggressively from this problem without giving it a moment's thought. I mean, for instance, did anyone play through the most recent Star Ocean? I couldn't weather more than twenty minutes of that game, despite the real-time combat, because the voices were so painful it almost sounded like they were making a parody of Star Ocean.
Anyway, like I said earlier, there are definitely worthwhile JRPGs out there, but there are pretty solid reasons not to like them.